<![CDATA[Chemistry concepts related to molecular structure are challenging to learn due to their abstract nature, the necessity for multiple representations, and the demand for three-dimensional spatial visualization skills. This study examines the implementation of Problem-Based Learning (PBL) supported by PhET Simulation, an interactive virtual tool that enables students to visualize and explore molecular structures and chemical concepts. The objective is to promote deep learning through meaningful, joyful, and mindful learning experiences. An embedded mixed-methods approach with a one-group pretest–posttest design was utilized. The sample consisted of 36 grade X students from SMA Negeri 3 Palopo, selected via random sampling. Research instruments included a conceptual understanding test, a joyful learning questionnaire, an observation sheet, and a PBL-based Student Worksheet (LKPD). Quantitative data were analyzed descriptively using N-Gain, with hypothesis testing conducted via the Wilcoxon Signed-Rank Test for meaningful learning and a paired-samples t-test for joyful learning. Qualitative data from student observations and reflections were analyzed thematically. The results showed a significant increase in meaningful learning (N-Gain = 0.554, moderate category) and joyful learning (N-Gain = 0.576, moderate category). Observations and thematic analysis further indicated that mindful learning developed to a high degree (80.5%), as evidenced by metacognitive awareness, conceptual reflection, monitoring of understanding, and scientific argumentation during problem solving. These findings indicate that integrating PBL and PhET Simulation enhances conceptual understanding and fosters a meaningful, enjoyable, and reflective learning experience, thereby supporting the development of deep learning characteristics.]]>
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